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Published May 31, 2021 | Version v1
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A report of 43 unrecorded bacterial species within the phyla Bacteroidetes and Firmicutes isolated from various sources from Korea in 2019

Creators

  • 1. Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, Yongin 17035, Republic of Korea
  • 2. School of Biosystem and Biomedical Science, Korea University, Seoul 02841, Republic of Korea
  • 3. Department of Microbiology, Chung-Ang University College of Medicine, Seoul 06973, Republic of Korea
  • 4. Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon 16419, Republic of Korea
  • 5. Department of Biotechnology, Hankyong National University, Anseong 17579, Republic of Korea
  • 6. Department of Bio & Environmental Technology, Seoul Women's University, Seoul 01797, Republic of Korea
  • 7. Department of Biology, Sunchon National University, Suncheon 57922, Republic of Korea
  • 8. Department of Microbiology, Chungnam National University, Daejeon 34134, Republic of Korea
  • 9. Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Republic of Korea & Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea & Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, Yongin 17035, Republic of Korea

Description

Kang, Heeyoung, Kim, Haneul, Yi, Hana, Kim, Wonyong, Yoon, Jung-Hoon, Im, Wan-Taek, Kim, Myung Kyum, Seong, Chi Nam, Kim, Seung Bum, Cha, Chang-Jun, Joh, Che Ok Jeon and Kiseong (2021): A report of 43 unrecorded bacterial species within the phyla Bacteroidetes and Firmicutes isolated from various sources from Korea in 2019. Journal of Species Research 10 (2): 117-133, DOI: 10.12651/JSR.2021.10.2.117

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Has part
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Is source of
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References

  • Alexander, S.K. and D. Strete. 2001. Microbiology: a photographic atlas for the laboratory. San Francisco, CA: Benjamin Cummings.
  • Brown, A.E. 2007. Benson's microbiological application laboratory manual in general microbiology, 10th edn. New York: McGraw-Hill.
  • De Vos, P., G.M. Garrity, D. Jones, N.R. Krieg, W. Ludwig, F.A. Rainey, K.-H. Schleifer and W.B. Whitman (editors). 2009. Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 3, The Firmicutes. New York: Springer.
  • Felsenstein, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. Journal of Molecular Evolution 17(6):368-376.
  • Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39(4):783.
  • Fitch, W.M. 1971. Toward defining course of evolution minimum change for a specific tree topology. Systematic Zoology 20(4):406-416.
  • Garcia-Lopez, M., J.P. Meier-Kolthoff, B.J. Tindall, S. Gronow, T. Woyke, N.C. Kyrpides, R.L. Hahnke and M. Goker. 2019. Analysis of 1,000 type-strain genomes improves taxonomic classification of Bacteroidetes. Frontiers in Microbiology 10:1-74.
  • Gupta, R.S. and S. Patel. 2019. Robust demarcation of the Family Caryophanaceae (Planococcaceae) and its different genera including three novel genera based on phylogenomics and highly specific molecular signatures. Frontiers in Microbiology 10:1-28.
  • Haakensen, M., C.M. Dobson, H. Deneer and B. Ziola. 2008. Real-time PCR detection of bacteria belonging to the Firmicutes Phylum. International Journal of Food Microbiology 125(3):236-241.
  • Haas, K.N. and J.L. Blanchard. 2020. Reclassification of the Clostridium clostridioforme and Clostridium sphenoides clades as Enterocloster gen. nov. and Lacrimispora gen. nov., including reclassification of 15 taxa. International Journal of Systematic and Evolutionary Microbiology 70(1):23-34.
  • Hahnke, R.L., J.P. Meier-Kolthoff, M. Garcia-Lopez, S. Mukherjee, M. Huntemann, N.N. Ivanova, T. Woyke, N.C. Kyrpides, H.-P. Klenk and M. Goker. 2016. Genome-based taxonomic classification of Bacteroidetes. Frontiers in Microbiology 7:1-37.
  • Janda, J.M. and S.L. Abbott. 2007. 16S rRNA gene sequencing for bacterial identification in the diagnostic laboratory: pluses, perils, and pitfalls. Journal of Clinical Microbiology 45(9):2761-2764.
  • Kim, H., J.H. Yoon, C.J. Cha, C.N. Seong, W.T. Im, K.Y. Jahng, C.O. Jeon, S.B. Kim and K. Joh. 2016. A report of 26 unrecorded bacterial species in Korea, belonging to the Bacteroidetes and Firmicutes. Journal of Species Research 5(1):166-178.
  • Koliada, A., G. Syzenko, V. Moseiko, L. Budovska, K. Puchkov, V. Perederiy, Y. Gavalko, A. Dorofeyev, M. Romanenko, S. Tkach, L. Sineok, O. Lushchak and L. Sineok. 2017. Association between body mass index and Firmicutes/Bacteroidetes ratio in an adult Ukrainian population. BMC Microbiology 17(1):1-6.
  • Krieg, N.R., W. Ludwig, J. Euzeby and W.B. Whitman. 2010. Phylum XIV. Bacteroidetes phyl. nov. Bergey's Manual of Systematic Bacteriology, 2nd edn. Edited by N.R. Krieg, J.T. Staley, D.R. Brown, B.P. Hedlund et al. New York, Springer 4:25.
  • Kumar, S., G. Stecher and K. Tamura. 2016. MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology and Evolution 33(7):1870- 1874.
  • Lane, D.J. 1991. 16S/23S rRNA sequencing. In: E. Stackebrandt and M. Goodfellow (eds.), Nucleic acid techniques in bacterial systematics, John Wiley & Sons, New York. pp. 115-175.
  • Ley, R.E., P.J. Turnbaugh, S. Klein and J.I. Gordon. 2006. Human gut microbes associated with obesity. Nature 444(7122):1022-1023.
  • Magee, C.M., G. Rodenheaver, M.T. Edgerton and R.F. Edlich. 1975. A more reliable Gram staining technique for diagnosis of surgical infections. American Journal of Surgery 130(3):341-346.
  • Nahar, S., D.H. Lee, J.W. Bae, W.T. Im, K.Y. Jahng, K. Joh, W. Kim, S.D. Lee, H. Yi and C.J. Cha. 2018. Report on 30 unrecorded bacterial species of the phylum Firmicutes isolated from Korea in 2016. Journal of Species Research 7(1):50-59.
  • Patel, S. and R.S. Gupta. 2020. A phylogenomic and comparative genomic framework for resolving the polyphyly of the genus Bacillus: Proposal for six new genera of Bacillus species, Peribacillus gen. nov., Cytobacillus gen. nov., Mesobacillus gen. nov., Neobacillus gen. nov., Metabacillus gen. nov. and Alkalihalobacillus gen. nov. International Journal of Systematic and Evolutionary Microbiology 70(1):406-438.
  • Pruesse, E., J. Peplies and F.O. Glockner. 2012. SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 28(14):1823-1829.
  • Russell, A.B., A.G. Wexler, B.N. Harding, J.C. Whitney, A.J. Bohn, Y.A. Goo, B.Q. Tran, N.A. Barry, H. Zheng, S.B. Peterson, S. Chou, T. Gonen, D.R. Goodlett, A.L. Goodman and J.D. Mougous. 2014. A type VI secretion-related pathway in Bacteroidetes mediates interbacterial antagonism. Cell Host & Microbe 16(2):227-236.
  • Saitou, N. and M. Nei. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4(4):406-425.
  • Sharmin, F., S. Wakelin, F. Huygens and M. Hargreaves. 2013. Firmicutes dominate the bacterial taxa within sugar-cane processing plants. Scientific reports 3:1-7.
  • Yoon, S.H., S.M. Ha, S. Kwon, J. Lim, Y. Kim, H. Seo and J. Chun. 2017. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. International Journal of Systematic and Evolutionary Microbiology 67(5):1613-1617.
  • Zheng, J., S. Wittouck, E. Salvetti, C.M.B. Franz, H.M.B. Harris, P. Mattarelli, P.W. O'Toole, B. Pot, P. Vandamme, J. Walter, K. Watanabe, S. Wuyts, G.E. Felis, M.G. Ganzle and S. Lebeer. 2020. A taxonomic note on the genus Lactobacillus: Description of 23 novel genera, emended description of the genus Lactobacillus Beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae.